Not another alternate universe
by Neferius
Summary: Nephilim; a being born of both Angel and Human DNA. Unbeknownst to Shinji Ikari, he happens to be one such being. With his father seeking retribution and a few Nephilim's seeking his affection. Can he survive the insanity? Asuka x Shinji x Rei
1. Yet another AU

**A/N: Let me just say that it's AU time and while everybody is altered they are still, at their core, the same. I'm also skipping some of the boring dialogue and events…cause their boring and used too damn much. **

**Remember I'm an AMATUER so don't expect a novel and since this is an AU OOC-ness will be happening and the pairings are gonna be interesting cause it's not what you think unless…well lets just say this might get a 'M' rating but I'm hoping to avoid that. Just let me know if I push 'T' too far later on.**

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**Not another alternate universe**

**Chapter One**

**Yet another AU**

'How'd I get into this situation' Thought Shinji Ikari as he was thrown into another building by the angel known as Sachiel. He once again didn't understand why he knew that was this creatures' name but right now he was more focused on not getting hit again. Unit 01 ducked behind a building to avoid a blast from the angel. 'And my day started out so well too' he sarcastically thought.

He had arrived here in the afternoon to meet with his father. He hasn't seen his father in more then a year and he could honestly say that he didn't miss him too much. His father had left him in the custody of an aunt and uncle of his back when Shinji was only eight. It was a sad day in his life but his father had told him that work would be so busy that he wouldn't of had the time to take proper care of him. Shinji got along okay with them and he barely ever saw his father during those years.

When he had first received a phone call from his dad telling him to meet him in Tokyo-3, he was unsure. Sure, he didn't hate the man but he also wasn't too fond of him either. The next day he had made his decision and had been on the next train to the city. He was told that a woman named Captain Katsuragi would be picking him up when he got there. The problem was she was more then an hour late and he was starting to get this uncomfortable feeling in his gut. Something wasn't right and he could feel it. He suddenly had the feeling of somebody watching him and he quickly turned around. What he saw left him frozen in place.

"Mo-mo-mother" standing just across the street was a teenage girl who, aside from her blue hair and red eyes, looked identical to his mother. He only had a few pictures of her from his uncle and he cherished them. She stared at him as he did the same to her. The stand off lasted until there was sudden explosion behind him that caught him off guard making him turn towards the direction of the loud sound. He quickly turned back around but the phantom girl had disappeared.

Shinji then felt a different presence coming his way. He looked towards the mountainside and coming into view was a giant humanoid monstrosity. The creature in question walked into the city and as if it sensed Shinji too it turned towards the small speck far below it.

"Sachiel" Shinji whispered and suddenly wondered why he knew that was this things name. As if hearing its name the creature lumbered over towards the lilim in front of him. Shinji was frozen stiff as the creature made its way towards him.

He heard the sound of a horn and then screeching tires coming from behind him. He whipped around to see a blue sports car and a lavender haired woman behind the wheel.

"Quick get in" She ordered him. He didn't argue with her and jumped into the car. Before he could even get his seat belt on the car bolted in the opposite direction of the monstrosity. They then drove off towards an unknown destination. While driving he could tell his savior was getting a little antsy so he decided to lighten the mood a little.

"So uh…my name is Shinji Ikari…what's yours," he nervously asked. She looked at him for a second. He looked a lot like the commander but she could tell that he must take after his mother.

"The names Katsuragi…but you can just call me Misato" She gave him a shy smile. She couldn't help it. She was always shy around new people but once she got to know them she would show her true self. She could tell it wouldn't take long with this boy.

"So your who I was supposed to meet up with earlier…but why are you so late" She was pretty late and if she would have been on time he wouldn't of had to stare down that monster.

"Well you see I kinda…ForgotToSetMyAlarmAndKindOfSleptInTooLate…sorry" She was truly embarrassed. What kind of Captain was she? She had a simple task and couldn't even get that right. Seeing that Misato truly was sorry made his slight annoyance go away.

"It's alright" He gave her a genuine smile that calmed her down a lot. After driving for a little while more Misato pulled out her cell phone and dialed a quick number.

"This is Captain Katsuragi here. Yes I have him with me. Yes he's in one piece. No I didn't. Look can you just get a car train ready for us? Can you make it an express this time? I'm really in a hurry…oh shut up Aoba" She hung up the phone and continued driving. They eventually arrived at the train cars and began their decent. Shinji spotted a logo all around them and had to ask.

"Nerv?" He looked at Misato.

"Yes, It's a secret organization under the control of the United Nations" was her answer back.

"And that's where my father is, right"?

"Of course…you do know what he does don't you"

"All he ever told me is that it was important for the future of all mankind" He answered back. Misato just nodded her head as the train car made it's way into the geo-front. "Whoa…it's a real geo-front" He said, amazed at what was right before him.

"That's right. This is our secret base of operations. Nerv headquarters" Misato told him "Yeah it's so secret that only those who work there, live in the city, or that have cable TV know that it exists". A little while later they were inside Nerv. They were lost but what's important is that they were there.

"What the Hell? Isn't this the right way" Misato was confused as she looked at the map "I'm still kind of getting used to the place". Shinji took a quick look at the map and struggled not to get angry.

"Umm Misato…your holding the map upside down" He pointed out.

"I wha…oops sorry" once again she had that truly sorry puppy dog look on her face "Well if we follow this here then…ah ha now I know where to go" Misato pointed out there direction and eventually made it to an elevator. Once inside they made their way even deeper into headquarters. Eventually stopping early letting in a blond woman in a swimsuit and lab coat combo.

"Where have you been Misato? I've been looking everywhere for you" The blond woman yelled "We are short on time you know" Misato let out a deep sigh.

"Sorry Rits" Ritsuko then notice the boy standing next to Misato

"So is this him," The doctor asked.

"Yep, he's the third according to the Marduk report".

"It's a pleasure to meet you, I'm Doctor Ritsuko Akagi" She put out her hand.

"Uh…hi. I'm Shinji Ikari," He said shaking her hand.

"Yep, he's just like his father. Minus the beard, grumpiness, and overall aura of pure tainted evil" Misato told her college friend.

"I can tell" Ritsuko chuckled and smiled at the boy.

As they made their way through some halls the communications system turned on. "Battle stations, Level one. Prepare for ground unit interception" Shinji heard what was said but was to distracted by what looked like a giant hand behind them.

"So how's Unit 01 doing?" Misato asked.

"It's currently undergoing refrigeration, using the B-type equipment," She answered back.

"Tell me Ritsuko, does it really work? It's never worked before, has it?"

"Actually Rei…" that name caught Shinji's attention but he didn't know why "…was able to synch with it a long time ago but could never activate it. The possibility of activation now is really slim"

"I guess it's a little late to say sorry it doesn't completely work" Misato joked. The group of three eventually made it to a rubber raft floating in a pinkish liquid. They got in and sped across the liquid. They reached the other end of the room and entered another smaller room. This room was very dark and Shinji had that feeling of being watched again. He turned to his side where he felt the eyes following him.

Again today he felt a strange presence. Before he could focus more on it the lights turned on showing a gigantic face staring right into his soul. Shinji yelped and jumped back a little. After taking a moment to calm down he spoke.

"A giant robot?" Ritsuko decided to finally speak up.

"This is man's ultimate fighting machine. The synthetic life form known as Evangelion, Unit 01. It has been built here in secret, it's mankind's last hope" Ritsuko looked kind of proud as she said it.

"Is this what my father's been doing all these years," Shinji thought out loud.

"Correct" Was heard above Shinji and the boy in question looked up "It's been too long Shinji" Gendo Ikari told his son. "We're moving out"

"Moving out? But Unit 00 is still in cryo-stasis, isn't it" Then it dawned on Misato why they were there "Wait a minute. You're going to use Unit 01"

"There's no other way Misato" Ritsuko told her friend.

"Now wait, Rei can't do it yet, can she? We don't have a pilot," Misato screamed.

"You just dropped one off" Ritsuko turned to Shinji and put her hand on his shoulder. "Shinji we need you to pilot Unit 01" Shinji was shocked. He didn't know the first thing about driving a car and even less about piloting a bio-weapon.

"But even Rei Ayanami took seven months to synchronize with her Eva and he just got here. It's impossible" Misato looked at her friend.

"Look the commander has faith in him and that's good enough for me" Shinji heard that and looked back up at his father.

"I…I don't think I can do this father. I…I" He stuttered.

"You must Shinji. There is no one else who can." Gendo told him.

"I've never even seen this thing before. There's no way I can pilot it" It was as he said that, that he felt a presence once again. Through all the yelling, screaming, and explosions outside no one heard the sound of an injured girl painfully hobbling towards them until she spoke up.

"I will pilot it" Her quiet voice was heard by all and when Shinji saw her he froze once again "I will pilot Unit 01," She once again stated.

"Rei you need to be in bed you still haven't fully recovered from your accident" Ritsuko told the young girl. Another loud explosion rocked the building and knocked down Rei. Shinji instinctively ran towards the struggling girl. As he reached her he could of swore he heard some one say 'look out'. He didn't realize anything till a giant hand came into his view protecting the children from falling debris above.

"The Eva activated itself," A male tech yelled out "It ripped out of the right arm restraint".

"That's…not possible. The entry plug isn't even inserted yet. That just can't happen" Ritsuko shouted.

Gendo just gave out a slight sigh of relief "Thank you, Yui".

Shinji lifted the blue haired girl in his arms 'Why do you look so much like mom' he thought. As he lifted her more he noticed she was bleeding. Ritsuko ran to the two teens and knelt down.

"Rei you'll get killed if you go out in that condition" Ritsuko turned to Shinji "You're the only one that can do it. If not for our sake, do it for Rei" Shinji looked into Rei's one good eye and in the back of his mind he knew he had to do it. He stood up and looked at his father.

"Fine. I'll pilot it" With those words still echoing in his head Shinji ducked under another blast from Sachiel. He was still getting used to this 'Eva' as they called it. It was surprisingly easy to move around. Two things he couldn't get used to though were the smell of blood and the creepy feeling of two different sets of eyes watching his every move.

"Synchronization at forty eight percent and holding" Maya Ibuki informed Misato.

"Good. We can do this" Misato told herself.

Back in the battle Shinji was shooting blanks when it came to ideas about taking this thing down.

"Do I have any weapons I can use?" He asked as his umbilical cord was severed.

"You have a Progressive Knife in your left shoulder. Just think of that weapon and its hatch should open" Ritsuko informed him.

"Got it" He heard something over the communicator about forty five seconds remaining but ignored it. 'Ok Shinji think…progressive knife progressive knife' he felt a pop on his arm and found what looked like a hilt of a knife. He grabbed the hilt and as he pulled it out a blade was released from the inside. "Cool" he said, like a child watching fireworks for the first time.

"Shinji, you only have twenty five seconds left before you batteries fail and Unit 01 deactivates. Hurry up and defeat that angel" Misato yelled.

"Crap" Shinji said as he dashed towards his ugly foe. Unit 01 jumped into the air and Shinji screamed as he brought the Prog Knife down on his enemy. There was a sudden orange flicker in front of him and he was stopped in an instant from his assault.

"An AT-Field" Ritsuko yelled.

Shinji landed hard onto the ground but was quickly back on his feet and charged again. And once again he was thrown back by the AT-Field.

"Shinji get out of there," Misato screamed as Unit 01 ran out of power.

Sachiel moved forward and grabbed Unit 01's head. It raised the mighty Evangelion off its feet and just stared at it.

Though he had no power left Shinji could still see what was going on and could feel the pain of being held by his head.

The rod on the back of Sachiel's elbow pulled back and the entire command crew could only watch in horror as the rod shot forward directly into Unit 01's right eye. Shinji screamed as he felt the continuing hammering being done to his right eye.

He felt like passing out but when he heard a voice in his head everything just disappeared. The voice was female but it was very violent and unfamiliar.

**"****Giving up already are you"** The voice said **"How pathetic"**

"Who are you" Shinji asked.

_"__Ignore her"_ another voice interrupted _"She just doesn't like to lose or get injured but then again who does"_ This other voice was almost heavenly but also sounded quite familiar _"Don't worry too much Shin-chan. All will be revealed soon. For now, just rest"_

As if under a spell, Shinji closed his eyes and fell into a deep sleep.

**"****Shall I or do you wish to take out Sachiel"** The dark voice asked.

_"Do as you wish. I have some time to make up"_

**"****More fun for me"** A sinister laugh was then heard.

Back on the command bridge, everyone just witnessed a hole be put through Unit 01's head.

"We've lost the signal from the entry plug. Pilots condition is unknown" Maya informed Ritsuko.

'This is not good. Unit 01 was our last line of defense' Ritsuko thought.

"Ma'am Unit 01 is reactivating".

"Impossible" Ritsuko looked back at the monitor.

Unit 01 began to rise to its feet. Sensing something wasn't right Sachiel turned around to see a foot heading right towards its face. It raised its AT-Field and stopped the assault by the purple abomination now standing before it.

Sachiel fired a blast from its eyes hoping to catch its foe off guard but Unit 01 simply ducked and then pounced towards Sachiel. The angel once again raised its AT-Field but this time Unit 01 punched right through the force field. Sachiel stumbled back as its AT-Field dissipated.

Unit 01, still equipped with its Prog knife, jumped onto Sachiel making it fall onto its back. Sitting on what many would call the angels stomach the Evangelion then raised the Prog knife in the air and halted its attack just long enough to release its jaw restraints and gave what many observers believed to be a smirk as it slammed the Progressive knife into the glowing core of the angel.

Sachiel squirmed as its core began to crack. Doing what any desperate creature that knew it was going to die would do, it wrapped it's arms and legs around Unit 01 and in an attempt to take it with it, Sachiel self destructed. The immense explosion engulfed Unit 01 and the surrounding buildings in a ball of fire.

A minute after the blast the video monitors picked up movement and zoomed in. Walking back towards Nerv was a very pleased looking Unit 01, its glowing eyes and gaping mouth just added to the effect.

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Shinji slowly woke up in a sterile white room. While opening his eyes he noticed that he could only see out of his left eye. Freaking out he sat up and grabbed towards his right eye. He winced as he touched it but felt bandages bound up around it. Remembering why he was there, he laid back down on the bed. 

"I guess that means I won…what the hell happened" He tried remembering what happened but all he remembered was the warm feeling of being held. He heard a knock on his door and looked up to see Misato walking towards him.

"How are you doing?" She shyly asked.

"Other then my eye quite well actually" Misato gave him a little smile but her smile faded as he asked a question "So what happened to Sach…I mean the angel?" Misato let out a breath and answered.

"You…well Unit 01 defeated it" Shinji gave her a confused look "After the angel pierced Unit 01's head we lost contact with you. Unit 01 then reactivated and, as if it were a wild animal, it caused a lot of damage making the angel self-destruct. We looked back at the data and have concluded that Unit 01 acted of its own accord. We don't yet know why it did it but I believe it was trying to protect you".

Shinji let it all sink in. He remembered the two voices inside Unit 01 and the feeling of being held. Just what was that thing he piloted? Noticing his dazed state Misato decided to change the subject.

"Well anyway the doctors said you'll be able to go home tomorrow but you'll have to wear that bandage over your eye for at least a week" Misato looked sadly at the boy 'You may never see out of that eye again' Shinji felt a now familiar presence and looked up at the door.

"Misato could you open the door please" He politely asked. She complied and as she opened it there stood Rei Ayanami with an embarrassed look on her face as she hand held up like she was just about to knock.

"Umm…Captain my sister wishes to speak with you".

"What could Ritsuko want now?" Misato asked.

"I was not given that information Captain" Rei answered.

"Very well. Could you keep an eye on Shinji till I get back"?

"Yes ma'am".

"Play nice Rei" Misato laughed as Rei squirmed uncomfortably. As Misato walked away Rei closed the door then locked it. Shinji didn't like that.

Not only did this girl look like his mother but also there was this odd feeling in his gut telling him to get close to her…like some kind of animal instinct. As Rei approached his bed he had the unnatural feeling of wanting to take her as his and frankly it was scarring the shit out of him. This wasn't like him. He didn't view women as a prize to be won or as a means to have mindless sex. But with Rei there was this inhuman urge that was pulling him towards her.

She sat on his bed and stared into his one good eye with her now fully healed eyes and from that look alone the urge was growing within him to jump her right here and now.

"My sister would not appreciate you doing that to me" She emotionlessly said but blushed at the thought.

"Wha…what do you mean" could she read his thoughts. Could she see right through him some how?

"You and I are the same. I feel exactly what you do right now and…it's…hard to control myself" Rei leaned forward a little. Shinji seeing this did the same. As they inched their way forward both knew they shouldn't but couldn't help it. Rei put her hand on Shinji's face and raised it up level to hers. They were both about to receive their first kiss…until the door burst open.

"Rei don't" Ritsuko yelled as she ran in.

Rei immediately stood up blushing like a tomato and Shinji, who was still in bed, wasn't any better off. Misato then came running into the room.

"Why the hell did you do that Rits"? Misato said while catching her breath

"No reason I just need to talk to these two…alone"

"No reason my ass. Your hiding something from me again aren't you" Misato crossed her arms and grunted.

"Misato just…oh hi Kaji" Misato squealed and turned around. Seeing nobody there she turned back around to see a door slam in her face.

"That was low Ritsuko" Misato angrily stomped away. Back in the room Ritsuko sat Rei down in a chair and turned towards Shinji.

"You were never told what happened to you before you born were you" Ritsuko asked. Shinji just looked at her.

"What do you mean? What happened to me?" He started to panic a little. Ritsuko put her hand on her shoulder to calm him down. It worked so she continued.

"It's not my right to tell you. That's something you'll have to ask your father. Now before you say anything let me tell you that, yes, I know you and Rei are being attracted to each other" Shinji was about to speak but Ritsuko wouldn't let him.

"Just listen to me okay. I have no problem with you two being together but you cannot be alone together. The urge will be too great and something bad may happen".

"Like what?" He asked.

"Look Shinji just try to stay calm around her okay. The same applies to you too Rei…don't act like I didn't see what you two were going to do" Rei and Shinji began to blush again "Now I suggest you get some sleep. Come along Rei, we need to get you home" Ritsuko walked out the door with Rei in tow. The blue haired girl looked back at Shinji and smiled briefly. Shinji smiled back as she turned and walked away. His smile quickly faded and he had to ask himself.

"What is happening to me"?

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**A/N: Story number five is online and wasting your time…wait that's not right. Anyway this just kinda started flowing out of me. I hope you liked it. The next chapter might be filler but I think it needs to be done…at least I hope or I'm screwed.**

**Review if you like.**

**Read ya Later**©.


	2. Truths Revealed

**A/N: Sorry, but it's time for some filler. This is to catch you up on what's going on in this world and reveal a little about a few peoples pasts. Don't worry since it's not all filler.**

**Any OOC-ness is on purpose…unless it's not. This is an AU after all.**

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**Not another alternate universe**

**Chapter Two**

**Truths Revealed**

It's been nearly a week since Shinji was hospitalized after his fight with the angel, known as Sachiel, and a lot has happened. He has moved in with Misato and learned that she was quite an organized person. Her apartment was a giant hurricane of a mess but it was an organized mess. She knew exactly where everything was and how much junk was on top of it. She also had a pet warm water penguin that drank beer and lived in a fridge…no, he never asked why.

Shinji and Rei had been spending a lot of time together, with Ritsuko keeping an eye on them, the whole week. He had learned quite a lot about the blue haired girl. She was pretty shy, quiet, and reserved but when on duty at Nerv she was very serious and assertive. Her adopted mother Naoko Akagi had raised her from infancy and after her death her daughter, Ritsuko Akagi, took Rei into her home as any sister would have. She has only two friends at school. A girl named Hikari Horaki and another named Mayumi Yamagishi.

Today could quite possibly be the most important part of this week for the young teenager as he was called into his fathers' office. He knocked on the giant metal doors and waited for a response. A simple 'come in' was given and the doors' magnetic locks disengaged. He walked into the cold and dark room. Sitting in the very middle behind a desk, with his fingers laced together, was his father. Standing behind him was an older man named Fuyutsuki with Ritsuko and Rei on both sides of the desk. He walked forward and became very nervous as he was told to sit down.

"Shinji" His father started "I'm sure you are well aware of a few changes within yourself lately".

"Ye…yes" Shinji stammered out. Ritsuko took this time to check up on a few things.

"Can you describe the changes for me please" She took out her pen and prepared to take notes.

"Well…you already know of my 'attraction' to Rei. I seem to know if she is nearby. I can sense when something bad is about to happen. Like Misato dropped her plate this morning and before I realized it, I had caught it" Ritsuko jotted a few things down.

"Anything else?"

"That's it…why is something seriously wrong with me" He was beginning to look a bit downcast.

"Shinji there is something I would like to be explained to you. It may be hard to hear but please just listen," Ritsuko said and Shinji simply nodded his head.

"Before you were born there were…complications".

"Like what?" Shinji asked while Ritsuko looked at her clipboard.

"Most of your internal organs were underdeveloped and you had a small hole in you left lung. Your mother ended up having a cesarean section and you were born…legally dead" Shinji found that he couldn't speak and just listened as Ritsuko continued.

"Your mother told us, before she went into surgery, that if anything bad had happen to you that you were to be put in cryo-stasis till she could help you" Shinji had a few tears in his eyes "Shinji this is where things get a little serious okay" He simply nodded once again.

"You should know that it was your mother that created the Evangelions but it was your father who perfected it" Shinji was a little shocked that his mother was involved "You see your mother was a scientist along side my mother here. Together they started an experiment called 'Project Ayanami'" Shinji took a quick glance at Rei and found her head down so their eyes could not meet.

"The experiment was to make a hybrid of a human and angel, an artificial Nephilim if you will" Shinji began to stare at Rei not believing what he was hearing. He saw a tear fall down her cheek.

"They used the DNA of the second angel, known as Lilith, and that of both my mother, Naoko Akagi and your mother, Yui Ikari. They combined them and after a year of experimentation they succeeded in their goal. The fetus of Rei Ayanami was born". Rei ran out of the office crying and Shinji was about to chase after her when he felt the strong hand of his father on his shoulder.

"Let her be" He said in a stern voice.

"But…".

"My sister has always been a little sensitive about her origins and I bet after spending some time with you she fears you rejecting her after hearing the truth. Don't worry, she'll be fine" Ritsuko reassured him.

"If you say so" Shinji was still a little worried and Ritsuko was glad that he didn't think badly of her sister.

"Now Shinji, I told you that so I could tell you that you and Rei are very much alike" Shinji looked up at the blond doctor "Like I told you, when you were born you were put into cyro-stasis until your mother could help you. With the success of 'Project Ayanami' your mother, along with the help of a German scientist by the name of Kyoko Soryu, was able to develop a way to put angel DNA into your already existing body. It took a few months of testing but they were able to infuse your body with angel DNA" Shinji began to get a little light headed and felt like he was about to throw up.

"I'll go get him some water," Fuyutsuki said as he walked towards the back of the room.

"Would you like me to stop Shinji? I know this is a lot to take in" Ritsuko was generally concerned for the boy.

"Just give me a minute to calm down please" Fuyutsuki handed him a glass of water "Thank you" Shinji slowly gulped it down. After he finished he just stared into his cup "So why am I only now being affected by my angel DNA?"

"I'll get to that" Ritsuko continued "The angel DNA was used to help your body recover from its lack of development. After you were revived you were simply meant to lead an ordinary life. Now we don't know too much about angel behavior but we do know that they can sense the presence of other angels or beings similar like a Nephilim. We first realized it when you and Rei were infants. By the way, she was born after you if you wanted to know" Shinji simply looked at the doctor…he actually was a little curious.

"We noticed that when you were brought to Nerv for testing that you tended to cry a lot and when you happened to pass by me holding my new baby sister you instantly stopped crying. But as your mother walked away you started back up. After some testing they realized that her mere presence calmed you down".

Shinji had felt calmness within himself whenever he was in the presence on Rei and hearing Ritsuko's words helped him realize that and a few things he had been thinking about as he got closer to the girl.

"You said earlier that Rei was made from some of the same DNA as my mother…does that make her…my sister" Shinji needed to know this. He didn't want his feelings to be mixed up. Ritsuko, in her mind, smiled at the boys' question. She always wanted her sister to have a boyfriend and Shinji could understand her on so many more levels then any other boy could.

"Actually, between a few random cells, my mothers DNA, your mothers, and that of the angel you are no more related to her then you are to Misato" A little smile cracked on Shinji's face as he heard that "Why were you wondering that Shinji" Ritsuko smirked as she seen the boys' embarrassed look.

"Uh…no reason…just curious" Shinji was glad to hear that she wasn't his sister. That thought grossed him out.

Ritsuko had then gone on to explain that there were two others his age that had dual DNA. One of them actually went to his school. It was Rei's friend Hikari.

Her parents worked for Nerv. More importantly her mother worked with Shinji's mother. Hikari had also been born with complications but the operation used on her was different. It was more perfected and therefore less angel DNA had to be used. Apparently she wouldn't have the 'Attractions' that plagued Rei and Shinji.

The other child was a pilot that lived in Germany named Asuka Langley Soryu. Her mother was a scientist at the German branch of Nerv and one of the researchers for 'Project Ayanami'. While Asuka was still a fetus in her mothers' womb she had been infused with the Angel DNA. The only difference with her was that it was from the first angel known as Adam.

Shinji had learned two things. The first is that should he ever come into contact with Asuka he was to make sure their blood didn't mix. The effects could be catastrophic. The second thing he learned was that the reason behind the human/angel hybrids, or Nephilim's as they were called, were to pilot the Evangelions.

This was the hardest thing to learn. The Evangelions were all made from the DNA of Adam except for his Unit 01, which had Lilith's instead. The Evangelions were living beings, much like Rei, but they required one thing to be able to function and this is where Shinji broke down.

The Evangelions required a human soul to tame the wild soul of the Eva itself. This fact was discovered too late, as each test pilot was absorbed into the Evangelion. Unit 00 and Unit 01 were tested at the same time and were piloted by Naoko Akagi and Yui Ikari. During their activation their sync scores rose to four hundred percent and the two women's souls had been absorbed.

At first everybody thought they had brain damage because the bodies existed and could recognize a few things and speak like four year olds. It wasn't until Unit 02's activation and Kyoko Zeppelin Soryu's soul was absorbed that they learned what truly happened. Sadly it was too late for the three women as one by one their bodies found ways to commit suicide.

"So my mother is alive inside of Unit 01," Shinji asked.

"Well, yes and no" Ritsuko answered, "Her soul is very much alive but she has lost her physical body".

"Is there anyway to get her soul out of it" Shinji was hopeful.

"Unfortunately no. We used cloned bodies of our mothers and tried to get the souls out and into the bodies but the souls are completely fused with the souls of the Evas" Shinji's face had a look of sadness to it. Ritsuko let out a small sigh "Project E has taken a lot from everybody, Shinji. All we can do is move on and not let the sacrifices go to waste" Gendo got up and walked up towards Shinji.

"Shinji, I know I have no right to call myself your father but…I would like to say that I'm proud of you my son" Gendo then silently walked out of his office leaving a teary eyed Shinji behind.

"You know he's not a bad as everyone labels him to be" Ritsuko walked up to Shinji and put her hand on his shoulder "He just has a very demanding job and has to make difficult decisions" Shinji looked up to a smiling Ritsuko "Come on, lets go take that bandage off you head" Shinji nodded and the two made their way out of the Commanders office. Fuyutsuki watched the two leave and sat in Gendo's chair.

"I sure hope he doesn't mind the…alteration we've made" The old teacher sat back in the chair and laughed "He'll probably think it's 'cool'"

* * *

Shinji sat on the examination table and swung his legs back and forth. Ritsuko said she'd be right back so Shinji just thought about his injury. 

"I remember Sachiel stabbing the Eva's eye and feeling my own eye in pain" he put his hand over his bandaged eye "I hope I'm okay. I mean it's been hurting a little but nothing too much" Ritsuko walked in with some scissors and her laptop.

"Okay, lets get started" She said as she sat at her computer and typed a few things. Shinji's right eye started hurting a bit so he spoke up.

"Hey Dr. Akagi, my eyes bugging me" He said as he closed his left eye in reaction to the pain.

"It's okay I figure that'd happen" Shinji opened his left eye and gave her a weird look. She then mumbled "Everything is online and working properly" She stood up and grabbed the scissors "All right Shinji things may seem a little bright at first but everything should be fine" Shinji just nodded his head as the doctor cut away the bandages then unwrapped them.

"Ah" Shinji winced as a bright white light engulfed his right eye. The brightness began to fade and pretty soon everything looked normal. Ritsuko to a light and flashed it into his eyes and he squinted. She then made him follow her pen with his eyes. After her little check up she spoke.

"Everything appears okay and the wireless Magi link is online," She said.

"Excuse me the whaty what what is online?" Shinji asked and Ritsuko looked away.

"You see Shinji…when you fought the angel your eye was kinda…pulverized".

"WHAT" Shinji screamed.

"Relax Shinji, you can see can't you" Shinji calmed down a little "We had a bio-cybernetic eye, similar to the Eva's eyes, implanted in its place" Shinji began shaking a little "Your eye is wirelessly linked to our Magi super computer and has a few interesting abilities that a normal eye doesn't…like infrared and a zoom feature" Shinji's shaking became noticeable and caught the doctors attention "Are you okay Shinji" the boy couldn't hold it in anymore.

"This is so cool" He squealed like a schoolgirl while Ritsuko just stared at him "I'm like a cybernetic super soldier" If Ritsuko knew Shinji then she would of known that he was into the whole sci-fi action movie thing.

"Your taking this better then I though" Shinji just smiled "That eye is still experimental so don't go telling people about it…not even Misato knows about it" Shinji nodded his head "Okay, the Magi control its functions so all you simply have to do is think it and the eye should do what you tell it as long as it has been programmed to do it. So no laser vision" Shinji's smile turned into a frown.

"Damn" he muttered.

"You'll get used to it" Ritsuko turned around to throw away the bandages. As she threw them in the trash one of the bandages didn't make it so Ritsuko bent over to pick it up. Shinji, like any teenage boy, stared at her backside. He squinted his eyes to get a closer look.

He then noticed in his right eye that her butt was getting bigger. He shook his head and the zoom deactivated **_"You enjoy your little peek"_** a female voice said. Shinji raised his head to see Ritsuko at her computer.

"You say something Doctor Akagi" The faux blonde turned to look at the boy.

"Uh no" She turned back around to her work.

"**_It wasn't her who spoke, boy,"_** The voice said. Shinji quickly looked behind him but nobody was there **_"Boo"_** Shinji jumped from the examination table, startling Ritsuko.

"Shinji what has gotten into you" Ritsuko asked as she got up.

"You tell me" he yelled "I'm hearing someone's voice in my head" Ritsuko looked at him strangely "And she seems like she's having fun with it" something finally clicked in Ritsuko's mind.

"Damn it mother," She swore as she typed a few commands into her computer.

**MAGI access granted: Online with Melchior, Casper, and Balthazar: Merging…merging complete.**

**Magi: Hello Ritsuko.**

**AkagiR: Mother, why did you hack into Shinji's eye?**

**Magi: I was bored. I do nothing but calculate all day. That's fine with Balthazar but Casper and Melchior wanted more. So we came up with a solution.**

Shinji noticed Ritsuko frown and growl. Whatever she was doing was irritating her.

**AkagiR: You do know Gendo won't allow this. He will have the eye removed and that will leave Shinji with only one good eye and we can't afford that.**

**Magi: Then don't tell him dear. Trust your mother. I wont do anything foolish. I will merely observe him. Besides, you could always use his eye as a communicator through me. Good-bye daughter.**

**AkagiR: Hey, I haven't even agreed that you cou**

**MAGI link terminated.**

"I never could have the last word could I mother" Ritsuko sighed and rubbed the bridge of her nose.

"Um Doctor…are you okay" Shinji asked as he walked up to her.

"I'm fine but now I need to tell you something else".

"Um…okay".

"Despite what most people think it was my mother that created the Magi" She started.

"Naoko was her name, right," he asked.

"Yes. It took her years to do it but she was able to create the Magi super computers. She found that using a human style of thought pattern in a computer would actually help it independently understand all incoming data and categorize it without being programmed to do so. Basically a self-learning computer" Shinji sat back onto the examination table as Ritsuko continued.

"She found a way to implant her own brain thought patterns into a digital form. To make the computer truly unique she actually made three different computers named Casper, Melchior, and Balthazar. Each had a personality of hers. Casper was her as a woman, Melchior was her as a mother, and Balthazar was her as a scientist. Each are different and can merge together to recreate my mother, digitally, to the day before the accident".

Shinji just sat intently listening to the story. He just found out he was part angel and pilots a sixty-meter tall bio-robot. Ritsuko's mom in the form of a computer was simple to understand for him.

"The problem is that she get bored easily. I can understand that but it seems implausible for a computer to 'feel' bored. I don't know if it really is her but I know when I talk to her that it sure seems like it. She got so bored that she hacked your eye so she could see through it and interact with you. She sees your eye we gave you as a way to see the world outside of the Magi" Shinji felt sorry for her mother…well at least the Magi that is.

"Will she…always be watching" He didn't want a woman, even a computer one, to see him shower, go to the rest room, or…um…his private time.

"I doubt it" Ritsuko smiled "If she wants to continue to see the world then nobody but us can know or the link will be terminated. Because of that she wont be online too much…I hope".

"I guess it's okay" Shinji said as he got up "Despite being a computer I do feel sorry for her".

"Thanks Shinji. Oh and by the way. Misato told me that you and Rei are going out to a movie tonight" Ritsuko smiled as Shinji became quite shy.

"Well I uh…I mean we decided to go have some fun and see that new 'Dragon Ball MBS' movie but that was before all of this info was thrown at me. She was so upset."

"Don't worry about it. I'll talk to her and she'll meet you there okay" Ritsuko put a reassuring hand on his shoulder.

"I will. Thanks doctor" Shinji opened the door.

"Call me Ritsuko, Shinji," She asked.

"Okay, thanks Ritsuko" He said as he closed the door. Ritsuko heard a ping noise on her laptop.

**Online with the MAGI.**

**Magi: You want me to keep an eye on them.**

**AkagiR: You just wanna see the movie, don't you.**

**Magi: Despite how bad it will be, yes I do.**

**AkagiR: Fine. Just let me know if they do anything their not supposed to.**

**Magi: Yes daughter.**

**MAGI link terminated.**

Ritsuko let out a sigh and closed her laptop.

"Just another fun day at the office"

* * *

Shinji was at the theaters at six o'clock just as they had planned but he couldn't find Rei. 

"Where is she? I hope she's coming" he talked to himself or so he thought.

**_"Don't worry my daughter will show up Shinji"_** The voice once again startled him.

"Don't do that".

**"_Sorry"_**.

"So what are you doing here"?

_**"What every mother wishes they could do"**_.

"And what is that"

**_"Watch their daughters first date"_**.

'Oh joy' Shinji thought. He felt a tapping on his shoulder. He turned around to see Rei in a light blue top and jeans.

"Hello…Shinji" She was nervous for multiple reasons "About earlier I…" Shinji cut her off.

"Don't worry about that Rei. Lets just go and enjoy the movie" Shinji held out his hand to her. Rei smiled and grabbed his hand.

Back in Nerv Maya Ibuki noticed the Magi processing power oddly fluctuate. If she really understood it she would of realized that the computer was simply happy.

* * *

**A/N: Well, there is chapter two. For all you Shinji x Rei fans I know your lovin' this. To all of you Shinji x Asuka fans you'll have to be a little patient for your turn.**

**In an effort to make this story more unique I'm actually merging about seven other story ideas into this. Though most will take effect later on, one of them is coming up.**

**Reviews are welcomed if you'd like to.**

**Until the next chapter…**

**Read ya Later.**


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